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Biology Project Server Policy
- Introduction
The Duke University Biology Department is seeing an increased interest in "Project Servers." These are typically high-end computers, running Linux, that are purchased by a research group to perform the tasks outlined in their project, e.g., Assembling the Fungal Tree of Life (AFTOL). This document will outline how these servers will be managed and maintained.
- Hardware Purchase
In order to adequately support multiple servers, the Biology Computer Team (BCT) requires Dell, rack-optimized servers. They will be housed in BioSci 323, which is a very small room. Therefore, the hardware must be approved by the BCT before purchase.
- Warranty and Hardware Maintenance
At the time of purchase, a manufacturer warranty should be included for three-five years. We recommend at least "Next Business Day Parts/Onsite", which is consistent with the priority that the BCT can offer to restore a malfunctioning server having hardware problems.
- Hardware Longevity
It is the responsibility of the project owner to replace the server at the end of the manufacturer warranty. Generally three to five years is considered a maximum useful life, but this will depend on the state of the hardware and software support. In any case it will not exceed the manufacturer warranty period.
- Basic Setup and Software Configuration
The basic operating system and software for the server will be installed by the BCT from Biology's mirror of the Duke University Linux Users Group (DULUG) Red Hat repository (i.e. "tree"). The Biology tree includes locally maintained packages familiar to biology users, e.g., AceDB, PHYLIP, and Biopython. Note this may not be the latest release of Linux. (E.g., Red Hat released Linux version 8.0 on September 30, 2002. However, as of February, 19, 2003, the most recent production release at Duke is version 7.3.)
Additional software in the Biology tree (e.g., a wide variety of databases, web server plug-ins, and scripting languages) may be installed by the project owner if approved by the BCT. Prior approval is necessary because some of this software is not allowed on the Biology Department network, e.g., Mail Relay, IRC, Usenet News, and Gnutella.
- Software Maintenance
The BCT will be responsible for regular operating system and software maintenance to the project server as security patches and updates are released.
Updates, backups, and other miscellaneous cron jobs will be scheduled to run automatically between 3:00 a.m. and 5:00 a.m. Many updates will be done using the Red Hat client, up2date, and the server, "Current." Also configuration files may be pushed out to servers via "Gromit" during this time. Project owners and users must not interfere with these jobs.
If maintenance involves downtime (i.e., the server is unavailable for normal use), it will typically be scheduled two weeks in advance. Less notice may be necessary depending on the risk of a particular security patch. The urgency of applying a patch will be determined in consultation with the Arts and Sciences Unix Team. Downtime may consist of only a short reboot required by a security patch or extend to a several hour downtime if an operating system upgrade is needed. The BCT will work with the project owner to coordinate the best time/day.
- Non-standard Software
Often the very reason for having the project server is to run software or services not provided by the department (e.g., custom applications, databases, and Zope). Within the bounds of security and reliability, the BCT will try to work with you to obtain and install this software. However, the limited resources available to the BCT do not allow us to configure nor become expert in every available package.
- Software Licenses
All software installed on the project server must be properly licensed. The project owner is responsible for any payment if required and will supply the BCT a copy of all licenses for the records.
- Non-standard Software in Packaged Form
If the project owner wants to install software that is in packaged form, i.e. as a "rpm," the BCT strongly recommends that you also request the source rpm to go with the package. This will allow the BCT to assist in debugging the software if there are problems installing it from the binary rpm.
- Non-standard Software in Unpackaged Form
Unpackaged software will typically be in the form of a "tar" file. The BCT has configured /usr/local as designated space where non-rpm software can be installed. Any project member can install software to this space (without administrative privileges), and this location is included in the backups of the project server.
- Administrative Privileges
Users may receive sudo access/administrative rights to the project server under the following conditions:
- Users become educated in and demonstrate competency on relevant issues.
- Users take responsibility for following standard procedures and guidelines associated with sudo access/administrative rights.
- Users follow standard written procedures for documenting the payment of any licensed software they install. See 8.
Request for sudo privileges can be made to the BCT via biocompute@duke.edu.
- Backups
The BCT will work with the project owner to determine how much data can reasonably be backed up. This will consist of a written agreement, so both the BCT and the project owner clearly understand what is being backed up. Nightly backups are held for at least 90 days, and monthly full backup tapes are held for six months. Permanent archives are the responsibility of the project owner. (Although the BCT can usually assist with the details and technology of these.)
- Network Usage
It is expected that project servers will behave as good "citizens" on the network and responsibly share the available network bandwidth for biology. If more network bandwidth is needed, we will have to make a special request to Duke OIT Data Communications.
- Documentation
The BCT highly recommends that the project owner require thorough documentation from the project programmers and that it be stored in usr/local/doc.
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